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The author presents a three degrees-of-freedom precision hybrid stage that can move and align an object on it for the measurement of its three-dimensional image using the confocal scanning microscope. The hybrid stage consists of two individually operating x - y - thetas stages, called the coarse stage and the fine stage. The coarse stage is driven by the three linear motors and produces the initial movement of an object. On the other hand, the fine stage is driven by the four voice coil motors and provides the final alignment of it with sub-micron metre accuracy. For control of the hybrid stage, a precision motion controller is proposed. The precision motion controller consists of a position and velocity control loop, an anti-windup compensator to eliminate the windup problem that occurs in the controller, a generator of optimal force, a precision position determiner to determine the exact position of the fine stage and a perturbation observer to observe the perturbation of the fine stage and compensate it. The performances of the precision motion controller of the hybrid stage are evaluated by experiment with a hardware setup.